Let's begin by looking at the actual paper (Aldrich and Maggert, 2014). Here's the abstract.

Heterochromatin is a significant component of the human genome and the genomes of most model organisms. Although heterochromatin is thought to be largely non-coding, it is clear that it plays an important role in chromosome structure and gene regulation. Despite a growing awareness of its functional significance, the repetitive sequences underlying some heterochromatin remain relatively uncharacterized. We have developed a real-time quantitative PCR-based method for quantifying simple repetitive satellite sequences and have used this technique to characterize the heterochromatic Y chromosome of Drosophila melanogaster. In this report, we validate the approach, identify previously unknown satellite sequence copy number polymorphisms in Y chromosomes from different geographic sources, and show that a defect in heterochromatin formation can induce similar copy number polymorphisms in a laboratory strain. These findings provide a simple method to investigate the dynamic nature of repetitive sequences and characterize conditions which might give rise to long-lasting alterations in DNA sequence.

The authors looked at highly repetitive DNA on the Drosophila melanogaster Y chromosome. Most of this DNA consists of multiple tandem copies of simple sequences like AAGAG, AATAT, or AAGAGAG. The number of copies in each block ranges from dozens to hundreds or even thousands. A lot of this DNA isn't included in published genomes because it's very difficult to determine the exact number of copies.

Aldrich and Maggert developed a PCR technique that allows them to estimate the number of copies of each repetitive sequence in a block. They discovered that different strains of Drosophila melanogaster have different numbers of copies of repetitive sequences. This is not news—it's exactly what you expect. But it's nice to have better data.

An obscure swatch of human DNA once thought to be nothing more than biological trash may actually offer a treasure trove of insight into complex genetic-related diseases such as cancer and diabetes, thanks to a novel sequencing technique developed by biologists at Texas A&M University.

The game-changing discovery was part of a study led by Texas A&M biology doctoral candidate John C. Aldrich and Dr. Keith A. Maggert, an associate professor in the Department of Biology, to measure variation in heterochromatin. This mysterious, tightly packed section of the vast, non-coding section of the human genome, widely dismissed by geneticists as "junk," previously was thought by scientists to have no discernable function at all.

The first thing you notice is that the press release talks about the human genome but the study focused on the small Y chromosome of Drosophila. In fairness, the abstract of the paper also mentions the human genome.

The second thing you might notice is that the repetitive sequences are dismissed as "junk" even though we've known for decades that much of it is part of the centromere and therefore required for chromsome segregation. That's not junk.

The third thing you notice is that there's no connection between what's published in the paper (on the Drosophila Y chromosome) and human diseases such as cancer and diabetes.

In the course of his otherwise routine analysis of DNA in fruit flies, Aldrich was able to monitor dynamics of the heterochromatic sequence by modifying a technique called quantitative polymerase chain reaction (QPCR), a process used to amplify specific DNA sequences from a relatively small amount of starting material. He then added a fluorescent dye, allowing him to monitor the fruit-fly DNA changes and to observe any variations.

Aldrich's findings, published today in the online edition of the journal PLOS ONE, showed that differences in the heterochromatin exist, confirming that the junk DNA is not stagnant as researchers originally had believed and that mutations which could affect other parts of the genome are capable of occurring.

"We know that there is hidden variation there, like disease proclivities or things that are evolutionarily important, but we never knew how to study it," Maggert said. "We couldn't even do the simplest things because we didn't know if there was a little DNA or a lot of it.

"This work opens up the other non-coding half of the genome."

It's true that the authors developed a clever technique to measure the number of repeats. But even though the block of sequence has a function, the exact number of copies is not fixed. That much has been known for a long time. If some of it is junk then it follows that during DNA replication you will invariably get deletions and duplications. Different populations will have variable numbers of repeats, although there's probably a minimum number that's required to maintain fitness.

This is what you expect and this is what they found. The press release makes it seem as though junk DNA was supposed to be "stagnant."

Maggert is quoted as saying, "This work opens up the other non-coding half of the genome." Highly repetitive DNA makes up about 1% of the human genome [What's in Your Genome]. By my rough calculation, that's 50 times less than half of the genome. I don't know what he means by "opens up."

Maggert explains that chromosomes are located in the nuclei of all human cells, and the DNA material in these chromosomes is made up of coding and non-coding regions. The coding regions, known as genes, contain the information necessary for a cell to make proteins, but far less is known about the non-coding regions, beyond the fact that they are not directly related to making proteins.

"Believe it or not, people still get into arguments over the definition of a gene," Maggert said. "In my opinion, there are about 30,000 protein-coding genes. The rest of the DNA -- greater than 90 percent -- either controls those genes and therefore is technically part of them, or is within this mush that we study and, thanks to John, can now measure. The heterochromatin that we study definitely has effects, but it's not possible to think of it as discrete genes. So, we prefer to think of it as 30,000 protein-coding genes plus this one big, complex one that can orchestrate the other 30,000."

I leave it to readers to draw their own conclusions.

In my opinion there are about 19,000 protein-encoding genes [How many genes do we have and what happened to the orphans?]. There may be as many as 10,000 other genes but Maggert seems to DEFINE genes as protein-encoding so those don't count. I agree that there's no perfect definition of a gene but most biologists accept the existence of genes that specify functional RNAs and most biologists don't include all regulatory sequences in their definition of a gene [see What Is a Gene?].

In light of the ENCODE publicity hype disaster and the subsequent debate, I'm surprised that a seemingly knowledgeable scientist would claim that 98% of the genome is required to "orchestrate" the known genes. We know that such a claim is almost certainly false.

Although other methods of measuring DNA are technically available, Aldrich notes that, as of yet, none has proven to be as cost-effective nor time-efficient as his modified-QPCR-fluorescence technique.

"There's some sequencing technology that can also be used to do this, but it costs tens of thousands of dollars," Aldrich said. "This enables us to answer a very specific question right here in the lab."

The uncharted genome sequences have been a point of contention in scientific circles for more than a decade, according to Maggert, a Texas A&M faculty member since 2004. It had long been believed that the human genome -- the blueprint for humanity, individually and as a whole -- would be packed with complex genes with the potential to answer some of the most pressing questions in medical biology.

Who were these scientists that believed the human genome was "packed with complex genes"? And what does this have to do with the Drosophila Y chromosome?

When human DNA was finally sequenced with the completion of the Human Genome Project in 2003, he says that perception changed. Based on those initial reports, researchers determined that only two percent of the genome (about 21,000 genes) represented coding DNA. Since then, numerous other studies have emerged debating the functionality, or lack thereof, of non-coding, so-called "junk DNA."

It's 2014. The debate is practically over. The three most important conclusions are:

Anyone who continues to refer to "non-coding" DNA as equivalent to "junk" DNA doesn't deserve to be taken seriously.

Now, thanks to Aldrich's and Maggert's investigation of heterochromatin, the groundwork has been laid to study the rest of the genome. Once all of it is understood, scientists may finally find the root causes and possibly treatments for many genetic ailments.

"There is so much talk about understanding the connection between genetics and disease and finding personalized therapies," Maggert said. "However, this topic is incomplete unless biologists can look at the entire genome. We still can't -- yet -- but at least now, we're a step closer."

I think it's time to stop issuing silly press releases that have nothing to do with the paper that's published. Usually we can blame the press office of the university but in this case the lead author is complicit. He should be ashamed of this performance.

15 comments
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Since one cannot infer any positional information from the qPCR data, I fail to see how this is a new "sequencing" method. But maybe I'm just being overly picky about semantics.

Also, "blueprint' is a facile description for the genome but it's not very accurate, as I think Martin describes nicely here: http://blogs.scientificamerican.com/sa-visual/2014/08/19/a-monkeys-blueprint/

I know very little about junk DNA... I admit it... but I'm willing to bet few bucks that gradually the so called junk DNA will be shrinking to the point that some people will be shamed to a point that they will have to retire....

"You know very little, but you're willing to bet any way. Truly you are an IDiot."

What do you know that you can prove about hydro-ventolgy you have been making so many claims about in regards to the origins of life...? Show me one successful experiment that you are smarter than hydro-vents, and I will take back all the unproven junk DNA stuff... well maybe except the puffer fish..... lol

I am continually conflicted about Science Daily. I use it as my browser home page b/c it provides a quick way to scan the latest science news. But I sure wish their people were less gullible about posting hype like this.

I do not think they claim to vet the press releases, they simply publish what they receive from academic sources. For anyone interested in biology, this blog performs a public service by doing the vetting. There appears to a recurring orientation to the press release bias, it appears calculated to appeal the perspective that biology should fit comfortably within a monotheistic framework.

Laurence A. Moran

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

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The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.